[BioC] [Bioc-sig-seq] Error in assign while calling the vmatchPattern function

Hervé Pagès hpages at fhcrc.org
Mon Jul 13 19:56:18 CEST 2009

Hi Jörn,

[cc'ing the mailing list]

Jörn Dietrich wrote:
> Hi all,
> I have the same problem by using the function getSeq() and I am using 
> the new release of R.
>  > sessionInfo() R version 2.9.1 (2009-06-26)
> x86_64-unknown-linux-gnu
> Does any one have an idea?

Unfortunately, some people are still experiencing this problem even
after they've upgraded to a recent version of R release/devel.

There was definitely a PROTECT/UNPROTECT bug in the reg.finalizer() code,
and that bug has been fixed in R release/devel one month ago. After
this fix, I did some (light) testing and was not able to get the
annoying 'formal argument "envir" matched by multiple actual arguments'
error anymore, so I concluded that the issue was solved...

Kasper contacted me off-list recently because he was still getting the
error. With the details he provided, I was able to isolate another
PROTECT/UNPROTECT issue, but this time in the setGeneric/setMethod
C code (methods package). I've sent a bug report to R-devel but haven't
heard back from them yet:


I'll post here again as soon as I have something new.

Thanks for your patience with this issue!


> Best wishes
> Joern

Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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E-mail: hpages at fhcrc.org
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